Phylogenetic, toxigenic and virulence profiles of Alternaria species causing leaf blight of tomato in Egypt

Three novel species of Alternaria (Pleosporales, Pleosporaceae) from cereal crops (Poaceae) in China

The genus Alternaria (Pleosporales, Pleosporaceae) comprises saprophytes and pathogens that are widespread around the world. Currently, more than 400 species are recognized within this genus and are classified into 29 sections. In this study, Alternaria strains were isolated from diseased leaves of two cereal crops, rice (Oryzasativa) and maize (Zeamays) in China. These Alternaria spp. were characterized by morphological characterization and phylogenetic analysis using maximum likelihood and Bayesian inference with multiple loci (ITS, GAPDH, RPB2, TEF1, Alt a 1, EndoPG, and OPA10-2). Based on the above analyses, three novel species of AlternariasectionAlternaria were introduced, namely A.oryzicola sp. nov., A.poae sp. nov., and A.zeae sp. nov. This study expands the species diversity of Alternaria associated with Poaceae plants in China.

Cyclobutrifluram Resistance in Alternaria alternata: Molecular Mechanisms and Detection Strategies

The resistance risk and mechanisms of cyclobutrifluram in Alternaria alternata are unclear. The baseline sensitivity of 111 A. alternata isolates to cyclobutrifluram was 0.10 ± 0.07 μg/mL. Eight cyclobutrifluram-resistant mutants of A. alternata were generated in the laboratory, exhibiting high-level and relative stable resistance. Cross-resistance was found between cyclobutrifluram and boscalid or pydiflumetofen, yet no cross-resistance was observed between cyclobutrifluram and iprodione, azoxystrobin, mefentrifluconazole, or difenoconazole. Each resistant mutant exhibited a reduced compound fitness index (CFI) compared to their parental isolates. An S73L substitution in AaSdhC or a P113T, H134N, or D145N mutation in AaSdhD conferred cyclobutrifluram resistance. Allele-specific PCR (AS-PCR) methods for the detection of mutations AaSdhCS73L, AaSdhDP113T, AaSdhDH134N, and AaSdhDD145N were successfully developed. In summary, A. alternata exhibits a moderate risk for developing resistance to cyclobutrifluram, attributed to the S73L substitution in AaSdhC or the P113T, H134N, or D145N mutations in AaSdhD, which are detectable using specific AS-PCR methods.

Haplotype diversity and phylogeny within Alternaria alternata and A. arborescens species complexes from tomatoes

Tomato (Solanum lycopersicum L.) is an economically important vegetable susceptible to various fungal diseases, including leaf spot caused by Alternaria spp. from the section Alternaria. In our study, a total of 72 tomato-associated Alternaria spp. strains from Latvia, Lithuania, Estonia, and Algeria were analysed by integrating morphological data, pathogenicity assay, multi-locus phylogeny, and haplotype assignment. Recovered Alternaria spp. strains were characterized by considerable variation in phenotypic diversity, non-pathogenicity to their host of origin and absence of the AAL-toxin biosynthesis gene (ALT1). Multi-locus phylogeny of the RNA polymerase II second largest subunit (rpb2), putative F-box-domain-containing protein (ASA-10), and putative histone-like transcription factor (ASA-19) confirmed the occurrence of both A. alternata and A. arborescens species complexes along with A. longipes and A. postmessia on symptomatic tomatoes. The discordant tree topology among single-gene phylogenies suggested the occurrence of potential recombination between phylogenetic lineages in the section Alternaria, resulting in putative alternata-arborescens and alternata-longipes hybrids. DNA polymorphism analysis of the rpb2, ASA-10, and ASA-19 loci revealed a high level of genetic diversity in the section Alternaria, and the number of single nucleotide polymorphisms (SNPs) and haplotypes varied among loci and lineages studied. A total of 16 and 6 multi-locus haplotypes were assigned in alternata and arborescens lineages, respectively. Global genetic diversity analysis of A. alternata and A. arborescens strains at the rpb2 locus confirmed that major haplotypes described from tomatoes were shared among other hosts of origin.

Functional diversity of the above-ground fungal community under long-term integrated, organic and biodynamic Vineyard Management

BACKGROUND

Sustainable agriculture increasingly emphasizes the importance of microbial communities in influencing plant health and productivity. In viticulture, understanding the impact of management practices on fungal communities is critical, given their role in disease dynamics, grape and wine quality. This study investigates the effects of integrated, organic, and biodynamic management practices on the diversity and function of fungal communities in a vineyard located in Geisenheim, Germany, focusing on above-ground parts such as bark, leaves, and grapes.

RESULTS

Our findings indicate that while overall fungal species richness did not significantly differ among management systems across various compartments, the composition of these communities was distinctly influenced by the type of management system. In particular, leaf and grape compartments showed notable variations in fungal community structure between integrated and organic/biodynamic management. No differences were observed between organic and biodynamic management. Integrated management demonstrated a significantly higher abundance of mycoparasites in comparison to organic and biodynamic management, primarily attributed to the increased presence of Sporobolomyces roseus, Sporobolomyces ellipsoideus and Rhodotorula glutinis.

CONCLUSIONS

The findings highlight the importance of management practices in shaping fungal community composition and function in vineyards. Although overall species richness remained unaffected, community composition and functional diversity varied, highlighting the potential for strategic microbiome management to enhance vineyard sustainability and plant health.

Three Alternaria Species, Including a New Species, Causing Leaf Spot Disease of Loquat (Eriobotrya japonica) in China

Loquat (Eriobotrya japonica) is an economically important subtropical fruit crop in China. Field surveys conducted in different loquat orchards located in Chongqing, Sichuan, and Fujian provinces between 2017 and 2020 resulted in a collection of 56 Alternaria-like isolates from trees exhibiting symptoms of loquat leaf spot. Multigene phylogenetic analyses using seven gene regions, namely, ITS, gapdh, RPB2, tef1, Alt a 1, endoPG, and OPA10-2, showed that all the isolates belonged to the genus Alternaria, and supporting morphological analysis identified them as members of species A. alternata, A. gaisen, and A. chongqingensis sp. nov. In vitro and in vivo pathogenicity tests showed all the identified species to be pathogenic and able to cause leaf spot disease on loquat. Moreover, comprehensive phylogenetic analyses employing all combinations of the above seven gene sequences revealed the capability of Alt a 1-tef1-endoPG to provide a well-resolved gene tree for Alternaria spp. at the species level. This study adds to the current knowledge on an unknown species (A. chongqingensis sp. nov.) and is the first report of A. gaisen in loquat worldwide.

Alternaria diseases on potato and tomato

Alternaria spp. cause different diseases in potato and tomato crops. Early blight caused by Alternaria solani and brown spot caused by Alternaria alternata are most common, but the disease complex is far more diverse. We first provide an overview of the Alternaria species infecting the two host plants to alleviate some of the confusion that arises from the taxonomic rearrangements in this fungal genus. Highlighting the diversity of Alternaria fungi on both solanaceous hosts, we review studies investigating the genetic diversity and genomes, before we present recent advances from studies elucidating host-pathogen interactions and fungicide resistances.

TAXONOMY

Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Pleosporales, Family Pleosporaceae, Genus Alternaria.

BIOLOGY AND HOST RANGE

Alternaria spp. adopt diverse lifestyles. We specifically review Alternaria spp. that cause disease in the two solanaceous crops potato (Solanum tuberosum) and tomato (Solanum lycopersicum). They are necrotrophic pathogens with no known sexual stage, despite some signatures of recombination.

DISEASE SYMPTOMS

Symptoms of the early blight/brown spot disease complex include foliar lesions that first present as brown spots, depending on the species with characteristic concentric rings, which eventually lead to severe defoliation and considerable yield loss.

CONTROL

Good field hygiene can keep the disease pressure low. Some potato and tomato cultivars show differences in susceptibility, but there are no fully resistant varieties known. Therefore, the main control mechanism is treatment with fungicides.

Characterization and toxicological potential of Alternaria alternata associated with post-harvest fruit rot of Prunus avium in China

Post-harvest fruit rot caused by Alternaria species is one of the most important threats to the fruit industry. Post-harvest rot on sweet cherry (Prunus avium) fruit was observed in the fruit markets of the Haidian district of Beijing, China. The fungal isolates obtained from the infected sweet cherry fruits matched the descriptions of Alternaria alternata based on the morphology and multi-gene (ITS, endo-PG, and Alta1) sequence analysis. Pathogenicity tests indicated that ACT-3 was the most virulent isolate, exhibiting typical post-harvest fruit rot symptoms. Physiological studies revealed that the optimal conditions for the growth of ACT-3 were temperature of 28°C, water activity of 0.999, and pH of 8 with 87, 85, and 86 mm radial growth of ACT-3 on a potato dextrose agar (PDA) medium, respectively, at 12 days post-inoculation (dpi). Moreover, the fungus showed the highest growth on a Martin agar medium (MAM) modified (85 mm) and a PDA medium (84 mm) at 12 dpi. The proliferation of the fungus was visualized inside the fruit tissues by confocal and scanning electron microscope (SEM), revealing the invasion and destruction of fruit tissues. Alternaria mycotoxins, tenuazonic acid (TeA), and alternariol (AOH) were detected in five representative isolates by HPLC analysis. The highest concentrations of TeA (313 μg/mL) and AOH (8.9 μg/mL) were observed in ACT-6 and ACT-3 isolates, respectively. This study is the first to present a detailed report on the characteristics and proliferation of A. alternata associated with sweet cherry fruit rot and the detection of toxic metabolites.

Small-spored Alternaria spp. (section Alternaria) are common pathogens on wild tomato species

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomatoes, several species cause early blight, leaf spots and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem in cultivated tomatoes, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.

Antifungal and antifeedant terpenoids from Paraphaeosphaeria sp. cultured by extract of host Ginkgo biloba

Five undescribed terpenoids including a polyketide-terpenoid hybrid paraphaone, and four eremophilane sesquiterpenoids, paraphaterpenes A-D, as well as two known compounds were isolated from the endophytic fungus Paraphaeosphaeria sp. cultured by extract of host Ginkgo biloba L. The structures were established by spectroscopic analyses, and the single-crystal X-ray diffraction. The antifungal activity of Paraphaeosphaeria sp. cultured by extract of G. biloba against the plant pathogen Alternaria alternata was significant and higher than that of PDB medium. Tested compounds indicated antifeedant activities against silkworms with feeding deterrence index at 10-70%. Paraphaone, paraphaterpenes A, C, D and alternariol methyl ether showed significant antifungal activities against the phytopathogens A. alternata, Aspergillus fumigatus, and entomopathogen Beauveria bassiana with MICs ≤4 μg/mL. And the preliminary structure-activity relationship of eremophilane sesquiterpenoids was exhibited. The culture of Paraphaeosphaeria sp. by host G. biloba medium afforded agricultural antibiotics.

Phylogenetic Analysis and Toxigenic Profile of Alternaria Species Isolated from Chickpeas (Cicer arietinum) in Argentina

Chickpeas are a very important legume due to their nutritional richness and high protein content and they are used as food for humans and as fodder for livestock. However, they are susceptible to fungal infections and mycotoxin contamination. The Alternaria genus was among the main fungi isolated from chickpea samples in Argentina. The species within this genus are able to produce several mycotoxins such as alternariol (AOH), alternariol monomethyl ether (AME), and tenuazonic acid (TA). So, the objectives of this study were to identify the Alternaria spp. found in the chickpea samples and to determine their toxigenic potential in vitro. A phylogenetic analysis of 32 Alternaria strains was carried out based on the combined sequences of the tef1, gpd, and Alt a1 genes. All Alternaria strains clustered into the section Alternaria and were identified as A. alternata and A. arborescens. Further, the toxigenic profile of each strain was determined in a ground rice–corn steep liquor medium and analysed by HPLC. Most strains were able to co-produce AOH, AME, and TA. These results indicate a potential risk for human health when consuming chickpeas since this legume could be contaminated with Alternaria and its mycotoxins, which are not yet regulated in food.

Alternaria alternata as endophyte and pathogen

Alternaria alternata is a common species of fungus frequently isolated from plants as both an endophyte and a pathogen. Although the current definition of A. alternata rests on a foundation of morphological, genetic and genomic analyses, doubts persist regarding the scope of A. alternata within the genus due to the varied symbiotic interactions and wide host range observed in these fungi. These doubts may be due in large part to the history of unstable taxonomy in Alternaria, based on limited morphological characters for species delimitation and host specificity associated with toxins encoded by genes carried on conditionally dispensable chromosomes. This review explores the history of Alternaria taxonomy, focusing in particular on the use of nutritional mode and host associations in species delimitation, with the goal of evaluating A. alternata as it currently stands based on taxonomic best practice. Given the recombination detected among isolates of A. alternata, different symbiotic associations in this species should not be considered phylogenetically informative.

Mycotoxin Profile and Phylogeny of Pathogenic Alternaria Species Isolated from Symptomatic Tomato Plants in Lebanon

The tomato is one of the most consumed agri-food products in Lebanon. Several fungal pathogens, including Alternaria species, can infect tomato plants during the whole growing cycle. Alternaria infections cause severe production and economic losses in field and during storage. In addition, Alternaria species represent a serious toxicological risk since they are able to produce a wide range of mycotoxins, associated with different toxic activities on human and animal health. Several Alternaria species were detected on tomatoes, among which the most important are A. solani, A. alternata, and A. arborescens. A set of 49 Alternaria strains isolated from leaves and stems of diseased tomato plants were characterised by using a polyphasic approach. All strains were included in the recently defined phylogenetic Alternaria section and grouped in three well-separated sub-clades, namely A. alternata (24 out of 49), A. arborescens (12 out of 49), and A. mali morpho-species (12 out of 49). One strain showed high genetic similarity with an A.limoniasperae reference strain. Chemical analyses showed that most of the Alternaria strains, cultured on rice, were able to produce alternariol (AOH), alternariol methyl ether (AME), altenuene (ALT) and tenuazonic acid (TA), with values up to 5634, 16,006, 5156, and 4507 mg kg⁻¹, respectively. In addition, 66% of the strains were able to co-produce simultaneously the four mycotoxins investigated. The pathogenicity test carried out on 10 Alternaria strains, representative of phylogenetic sub-clades, revealed that they were all pathogenic on tomato fruits. No significant difference among strains was observed, although A. alternata and A. arborescens strains were slightly more aggressive than A. mali morpho-species strains. This paper reports new insights on mycotoxin profiles, genetic variability, and pathogenicity of Alternaria species on tomatoes.

Species diversity, novel interactions and absence of well-supported host-guided phylogenetic groupings of Neotropical Alternaria isolates causing foliar lesions in Solanaceae

AIM

To report the characterization of 120 Alternaria isolates inducing early blight-like foliar lesions in nine species of five Solanaceae genera collected across all macrogeographical Brazilian regions.

MATERIAL AND RESULTS

Phylogenetic relationships were assessed via analyses of the Alternaria alternata allergenic protein-coding, glyceraldehyde-3-phosphate dehydrogenase and the calmodulin gene sequences. Most of the tomato isolates were placed into the Alternaria linariae cluster, whereas most of the potato isolates were grouped with Alternaria grandis. Novel host-pathogen interactions were also reported. Seventeen isolates were selected for morphometrical characterization, and a subsample of 13 isolates was employed in pathogenicity assays on tomato, potato, eggplant, scarlet eggplant, Capsicum annuum, Datura stramonium, Physalis angulata and Nicotiana tabacum. Eleven isolates were able to induce foliar lesions in tomatoes but none in C. annuum. Potato was susceptible to a subgroup of isolates but displayed a subset of isolate-specific interactions. Morphological traits were in overall agreement with molecular and host range data.

CONCLUSION

Alternaria linariae and A. grandis were confirmed as the major causal agents of tomato and potato early blight, respectively. However other Alternaria species are also involved with early blight in solanaceous hosts in Brazil.

SIGNIFICANCE AND IMPACT OF THE STUDY

The diversity and host-specific patterns of the Alternaria isolates from Solanaceae may have practical implications in establishing effective early blight genetic resistance and cultural management strategies especially for tomato and potato crops.